ORCID Profile
0000-0003-2593-0303
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Aquaculture | Manufacturing Processes and Technologies (excl. Textiles) | Fisheries Sciences | Fish Physiology and Genetics
Publisher: Elsevier BV
Date: 09-2006
Publisher: Cold Spring Harbor Laboratory
Date: 28-12-2021
DOI: 10.1101/2021.12.28.474260
Abstract: Nocardia seriolae has caused significant fish losses in Asia and the Americas in recent decades, including in Vietnam, which has witnessed devastating economic and social impacts due to this bacterial pathogen. Surveillance strategies are urgently needed to mitigate N. seriolae dissemination in Vietnamese aquaculture and mariculture industries. Whole-genome sequencing (WGS) offers the highest level of resolution to discriminate closely related strains and to determine their putative origin and transmission routes. However, WGS is impractical for epidemiological investigations and pathogen surveillance due to its time-consuming and costly nature, putting this technology out-of-reach for many industry end-users. To overcome this issue, we targeted two previously characterised, phylogenetically informative single-nucleotide polymorphisms (SNPs) in N. seriolae that accurately distinguish: i) Vietnamese from non-Vietnamese strains, and ii) the two Vietnamese subclades. Using the mismatch lification mutation assay (MAMA) format, we developed assays that genotype strains based on differences in licon melting temperature (melt-MAMA) and size (agarose-MAMA). Our MAMA assays accurately genotyped strains both from culture and fish tissues at low cost, using either real-time (~AUD$1 er s le) or conventional (~AUD$0.50 er s le) PCR instrumentation. Our novel assays provide a rapid, reproducible, and cost-effective tool for routine genotyping of this pathogen, allowing faster identification and treatment of nocardiosis-effected permit fish within Vietnamese aquaculture/mariculture facilities, an essential step in mitigating N. seriolae -associated losses.
Publisher: Springer Science and Business Media LLC
Date: 19-02-2016
DOI: 10.1038/SREP21486
Abstract: This study assessed whether selection for high growth in a challenging environment of medium salinity produces tilapia genotypes that perform well across different production environments. We estimated the genetic correlations between trait expressions in saline and freshwater using a strain of Nile tilapia selected for fast growth under salinity water of 15–20 ppt. We also estimated the heritability and genetic correlations for new traits of commercial importance (sexual maturity, feed conversion ratio, deformity and gill condition) in a full pedigree comprising 36,145 fish. The genetic correlations for the novel characters between the two environments were 0.78–0.99, suggesting that the effect of genotype by environment interaction was not biologically important. Across the environments, the heritability for body weight was moderate to high (0.32–0.62), indicating that this population will continue responding to future selection. The estimates of heritability for sexual maturity and survival were low but significant. The additive genetic components also exist for FCR, gill condition and deformity. Genetic correlations of harvest body weight with sexual maturity were positive and those between harvest body weight with FCR were negative. Our results indicate that the genetic line selected under a moderate saline water environment can be cultured successfully in freshwater systems.
Publisher: Elsevier BV
Date: 05-2015
Publisher: Elsevier BV
Date: 05-2014
Publisher: Public Library of Science (PLoS)
Date: 18-02-2013
Publisher: Elsevier BV
Date: 05-2014
Publisher: Cold Spring Harbor Laboratory
Date: 12-2021
DOI: 10.1101/2021.11.30.470482
Abstract: Between 2010 and 2015, nocardiosis outbreaks caused by Nocardia seriolae affected many permit farms throughout Vietnam, causing mass fish mortalities. To understand the biology, origin, and epidemiology of these outbreaks, 20 N. seriolae strains collected from farms in four provinces in the South-Central Coast of Vietnam, along with two Taiwanese strains, were analysed using genetics and genomics. Pulsed-field gel electrophoresis identified a single cluster amongst all Vietnamese strains that was distinct from the Taiwanese strains. Like the PFGE findings, phylogenomic and single-nucleotide polymorphism (SNP) genotyping analyses revealed that all Vietnamese N. seriolae strains belonged to a single, unique clade. Strains fell into two subclades that differed by 103 SNPs, with almost no ersity within clades (0-2 SNPs). There was no association between geographic origin and subclade placement, suggesting frequent N. seriolae transmission between Vietnamese mariculture facilities during the outbreaks. Vietnamese strains shared a common ancestor with strains from Japan and China, with the closest strain, UTF1 from Japan, differing by just 217 SNPs from the Vietnamese ancestral node. Draft Vietnamese genomes range from 7.55-7.96 Mbp in size, have an average G+C content of 68.2%, and encode 7,602-7,958 predicted genes. Several putative virulence factors were identified, including genes associated with host cell adhesion, invasion, intracellular survival, antibiotic and toxic compound resistance, and haemolysin biosynthesis. Our findings provide important new insights into N. seriolae epidemiology and pathogenicity and will aid future vaccine development and disease management strategies, with the ultimate goal of nocardiosis-free aquaculture.
Publisher: Elsevier BV
Date: 08-2015
DOI: 10.1016/J.MARGEN.2015.04.006
Abstract: The banana shrimp Fenneropenaeus merguiensis is a commercially important marine crustacean for world aquaculture and fisheries. Despite this, limited genetic information is available for it and many other penaeid shrimp species. Here we present the first in-depth analysis of the transcriptional content of 8 different tissues from the banana shrimp using RNA-Seq technologies. A total of over 1 million single-end and over 49 million paired-end reads were obtained from Roche 454FLX and illumina sequencing platforms, respectively, resulting in an assembly of 124,631 transcripts with an N50 of 1,332 and mean length of 514 nt. A total of 59,179 putative protein sequences obtained from the assembled transcripts were annotated using public protein sequence databases and assigned 20,430 BLAST hits, 16,866 GO terms and 13,304 KOG categories. Further analysis revealed a rich set of transcript sequences exhibiting homology with genes associated with reproduction, sex determination and development and distinguished the tissues responsible for this expression. This report adds a substantial contribution to the sequence data currently available for F. merguiensis, providing valuable resources for further research.
Publisher: Informa UK Limited
Date: 1994
DOI: 10.3109/10425179409039713
Abstract: The cDNA encoding the preprotein growth hormone from the dolphinfish (Coryphaena hippurus) has been cloned and sequenced. The cDNA was derived by reverse transcription of RNA from the pituitary of a young fish using the method known as Rapid Amplification of cDNA Ends (RACE). An oligonucleotide primer corresponding to the 5' region of Pagrus major and the universal RACE primer enabled lification using the Polymerase Chain Reaction (PCR). The dolphinfish and yellow-tail, Seriola quineqeradiata, are both members of the sub-order Percoidei (Perciforme) and their GH sequences show a high level of homology.
Publisher: Elsevier BV
Date: 04-2014
Publisher: Elsevier BV
Date: 10-2017
Publisher: Elsevier BV
Date: 06-2016
Publisher: Hindawi Limited
Date: 22-11-2016
DOI: 10.1111/ARE.13227
Publisher: Elsevier BV
Date: 03-2016
Publisher: Elsevier BV
Date: 09-2007
Publisher: Hindawi Limited
Date: 17-07-2016
DOI: 10.1111/ARE.12530
Publisher: Springer Science and Business Media LLC
Date: 12-2014
Publisher: Springer Science and Business Media LLC
Date: 07-09-2016
Publisher: Springer Science and Business Media LLC
Date: 05-1993
DOI: 10.1007/BF00281608
Abstract: This pilot study explored the feasibility, acceptability, and usability of a web-based intervention for survivors of physical inactivity-related cancers through a two-arm, 12-week randomized controlled trial. Secondarily, this study tested the change in physical activity (PA) and sedentary time with intervention exposure. Prior to randomization to the intervention (n = 45) or behavior "as usual" wait-listed control (n = 40) groups, participants completed baseline surveys and an accelerometer protocol. The intervention focused on increasing PA and decreasing sedentary time through social cognitive theory techniques. Follow-up acceptability/usability surveys (intervention group only) and accelerometers were sent after the intervention period. Information on intervention completion, adverse events, and user statistics were collected to determine feasibility. Median login time and mean acceptability/usability scores were calculated. Participants (mean age = 60 ± 7 years) included female (n = 80, 94%) and male survivors of breast (82%), colon (6%), endometrial (6%), bladder (4%), and kidney (2%) cancer. Seventy-eight (91.7%) participants returned partially or fully complete post-intervention data. There were no reported injuries or safety concerns. Intervention participants logged into the website for a total of 95 min (Q1, Q3 = 11, 204). System usability scores (72 ± 3) indicated above average usability of the website. Changes in time spent active and sedentary were not statistically significantly different between groups (p = 0.45), but within-group changes suggested intervention group participants spent more time active and less time sedentary after the intervention. Results of this pilot study suggest its feasibility and acceptability for survivors of several inactivity-related cancers. Additional research to determine long-term efficacy is warranted. This low-cost online-only intervention has the potential to have a very broad reach. Clinical Trials Number: NCT03983083. Date registered: June 12th, 2019.
Publisher: Hindawi Limited
Date: 07-2004
Publisher: Elsevier BV
Date: 2018
Publisher: Elsevier BV
Date: 09-2006
Publisher: Elsevier BV
Date: 06-2013
Publisher: Elsevier BV
Date: 05-2004
Publisher: Elsevier BV
Date: 02-2016
Publisher: Elsevier BV
Date: 06-2015
DOI: 10.1016/J.JIP.2015.05.002
Abstract: Hepatopancreatic parvo-like virus (HPV) has been reported from a variety of shrimp species around the world, including Australia, and thought to impact negatively on production, but until now there was scant information available on variation of HPV over time, ponds and shrimp lineages or families, information that could be used to manage or reduce virus levels. Here we report HPV copy number estimated using qPCR from 1500 in idual shrimp s led over three years and encompassing 91 ponds, 21 breeding groups or lineages and 40 families. HPV copy number variation between ponds was used by farm management as a criterion to choose prospective broodstock (candidates were taken from low HPV ponds). Despite such choice, HPV levels in farmed animals were not reduced from 2011 to 2013. Accordingly, the hypothesis that HPV levels can be reduced over time simply by considering average HPV levels in ponds alone is rejected. Different lines of shrimp within the same farm had different HPV levels, but as lines were raised separately, the line differences could be due to either genetic or environmental differences, the latter including possible different rearing effects and differences in vertical transmission. There were large (up to 2-3 LOG fold) differences of HPV levels between families bred and grown together contemporaneously, and the heritability for HPV copy number was estimated to be moderate to large (0.40 ± 0.13). Apart from genetic differences, differences of vertical transmission from dams may contribute to the between family differences, in any case we postulate that selection between families could be an effective method to reduce HPV levels. HPV levels were not genetically correlated with performance traits such as body weight or length, so selection for HPV level should not adversely affect production characteristics. This is the first evidence for an aquacultured species that viral levels, as opposed to survival/resistance to viruses, may have a substantial host genetic component. The heritability reported here for virus copy number was higher that most heritabilities reported for survival to specific pathogens such as white spot, raising the general postulate that selection for virus copy number may be more effective and repeatable than selection for survival to pathogen challenge.
Publisher: Wiley
Date: 16-02-2016
DOI: 10.1111/JFD.12348
Abstract: The main aim of this study was to estimate the heritability for four measures of deformity and their genetic associations with growth (body weight and length), carcass (fillet weight and yield) and flesh-quality (fillet fat content) traits in yellowtail kingfish Seriola lalandi. The observed major deformities included lower jaw, nasal erosion, deformed operculum and skinny fish on 480 in iduals from 22 families at Clean Seas Tuna Ltd. They were typically recorded as binary traits (presence or absence) and were analysed separately by both threshold generalized models and standard animal mixed models. Consistency of the models was evaluated by calculating simple Pearson correlation of breeding values of full-sib families for jaw deformity. Genetic and phenotypic correlations among traits were estimated using a multitrait linear mixed model in ASReml. Both threshold and linear mixed model analysis showed that there is additive genetic variation in the four measures of deformity, with the estimates of heritability obtained from the former (threshold) models on liability scale ranging from 0.14 to 0.66 (SE 0.32-0.56) and from the latter (linear animal and sire) models on original (observed) scale, 0.01-0.23 (SE 0.03-0.16). When the estimates on the underlying liability were transformed to the observed scale (0, 1), they were generally consistent between threshold and linear mixed models. Phenotypic correlations among deformity traits were weak (close to zero). The genetic correlations among deformity traits were not significantly different from zero. Body weight and fillet carcass showed significant positive genetic correlations with jaw deformity (0.75 and 0.95, respectively). Genetic correlation between body weight and operculum was negative (-0.51, P < 0.05). The genetic correlations' estimates of body and carcass traits with other deformity were not significant due to their relatively high standard errors. Our results showed that there are prospects for genetic selection to improve deformity in yellowtail kingfish and that measures of deformity should be included in the recording scheme, breeding objectives and selection index in practical selective breeding programmes due to the antagonistic genetic correlations of deformed jaws with body and carcass performance.
Publisher: Oxford University Press (OUP)
Date: 28-01-2016
Abstract: Here we report a newly identified 'Chalky back' phenomenon in banana prawns (Fenneropenaeus merguiensis) farmed in North Queensland, Australia. This was characterized by localized white discoloured segmentation of the cervical groove, moreover, after cooking the prawns exploded, making them unfit for commercial sale. Histological examination revealed breakdown of gut and abdominal muscle tissue in some moribund specimens. We selectively isolated Vibrio spp., which are known prawn pathogens, from healthy and Chalky back specimens. Isolated bacteria were identified, typed and tested for the presence of eight virulence genes (VGs), biofilm formation, adherence and cytotoxicity to fish cells. In all, 32 isolates were recovered and identified as Vibrio harveyi, V. owensii, V. sinaloensis-like, V. c bellii, V. shilonii, Vibrio sp. and Photobacterium damselae using 16S rRNA gene sequencing. All V. harveyi carried VGs coding for haemolysin, toxR and flagella formed biofilm and adhered to both cell lines. This was similar to the V. sinaloensis-like strains that were only isolated from Chalky back specimens. Our data suggest that Vibrio spp. may play a role in the pathogenesis of Chalky back. This study is the first report of Chalky back phenomenon in farmed banana prawns that needs to be closely monitored by the industry.
Publisher: Ivyspring International Publisher
Date: 2012
DOI: 10.7150/IJBS.3517
Publisher: Elsevier BV
Date: 09-2018
Publisher: Elsevier BV
Date: 06-2013
Publisher: Microbiology Society
Date: 04-07-2022
Abstract: Between 2010 and 2015, nocardiosis outbreaks caused by Nocardia seriolae affected many permit farms throughout Vietnam, causing mass fish mortalities. To understand the biology, origin and epidemiology of these outbreaks, 20 N . seriolae strains collected from farms in four provinces in the South Central Coast region of Vietnam, along with two Taiwanese strains, were analysed using genetics and genomics. PFGE identified a single cluster amongst all Vietnamese strains that was distinct from the Taiwanese strains. Like the PFGE findings, phylogenomic and SNP genotyping analyses revealed that all Vietnamese N. seriolae strains belonged to a single, unique clade. Strains fell into two subclades that differed by 103 SNPs, with almost no ersity within clades (0–5 SNPs). There was no association between geographical origin and subclade placement, suggesting frequent N. seriolae transmission between Vietnamese mariculture facilities during the outbreaks. The Vietnamese strains shared a common ancestor with strains from Japan and China, with the closest strain, UTF1 from Japan, differing by just 220 SNPs from the Vietnamese ancestral node. Draft Vietnamese genomes range from 7.55 to 7.96 Mbp in size, have an average G+C content of 68.2 % and encode 7 602–7958 predicted genes. Several putative virulence factors were identified, including genes associated with host cell adhesion, invasion, intracellular survival, antibiotic and toxic compound resistance, and haemolysin biosynthesis. Our findings provide important new insights into the epidemiology and pathogenicity of N. seriolae and will aid future vaccine development and disease management strategies, with the ultimate goal of nocardiosis-free aquaculture.
Publisher: Elsevier BV
Date: 07-2004
No related organisations have been discovered for Wayne Knibb.
Start Date: 2014
End Date: 12-2019
Amount: $5,000,000.00
Funder: Australian Research Council
View Funded Activity